Supplemental Material for de Lima, Hanlon, and Gerton, 2020

<p>Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The <i>1.688</i>satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in <em>Drosophila melanogaster</em>and has been linked to several different biological functions. We investigated the presence and evolution of the <i>1.688</i>satDNA in 16 <i>Drosophila</i>genomes. We find that the <i>1.688</i>satDNA family is much more ancient than previously appreciated, being shared amongst part of the <i>melanogaster</i>group that diverged from a common ancestor ~27 Mya. We found that the <i>1.688</i>satDNA family has two major subfamilies spread throughout <i>Drosophila</i>phylogeny (~360 bp and ~190 bp). Phylogenetic analysis of ~10,000 repeats extracted from 14 of the species revealed that the <i>1.688</i>satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the <a></a><a><i>1.688</i>satDNA </a>as the most perduring satDNA family described in <i>Drosophila</i>phylogeny to date. Our study provides a strong foundation for future work on the functional roles of <i>1.688</i>satDNA across many <i>Drosophila</i> species.</p>